After about 3 months off Agents of SHIELD returns pretty much where we left off. But we open up in 1983 and we see a young boy teleporting around in a room. This boy, Gordon, has no eyes, it is the same boy that grows up to be the man we saw in the coda of the show’s winter.
To comfort Gordon is Skye’s mom, Jiaying. It seems that Jiaying has been doing this for quite some time now to others that have gone through the same alien mist that Raina and Skye went through.
Back to the present day, Skye is in quarantine and is feeling really guilty over Tripp’s death but Coulson says that Tripp was a hero for trying to save her and stopping the city from getting in the hands of HYDRA. We also learn that Mack is going to be alright after having the alien city take over his body to do its bidding. Later, Bobbi visits Skye to give her some quarantine survival stuff like magazines, headphones and a can of Cactus juice or something like that.
Everyone at SHIELD is coping with Tripp’s death in their own way while Fitz is working getting Skye’s biometric/fitbit like device to work again so they can see what her internal readings where when the earthquake happened. Fitz does get frustrated over not being able to fix it and asks how Mack is doing. Mack says that he will be okay and when Fitz says he understands what he is going through, Mack believes he doesn’t but he really does.
Back in Puerto Rico, Simmons is investigating the alien city and the rubble left behind and later will flood the city, on Coulson’s orders. Complicating matters is a newly transformed Raina who attacks several of the scientists, killing some and leaving others in critical condition. Simmons manages to get some shots off at Raina and brings back some blood samples to examine.
Raina’s transformation did not go as planned and when she confronts Cal about it, we see her remove her hood and she is covered in thorns. Cal said that Raina wanted this but she counters that Skye took her transformation away from her. When Cal hears that Skye/Daisy came away unscathed but transformed, he is elated and believes that she will come to him once SHIELD starts to reject her. Raina wants Cal to help her but he tells her that she is on her own and if she wants to end her suffering then she has to kill herself.
Elsewhere, we see some HYDRA head council get together that consists of characters that sound like they could be new suspects in Clue 2.0. We have the banker, the Sheik and the Baroness meeting with Dr. List and Bloom about who should take over now that Whitehall is dead. The group believe that Bakshi is the ideal candidate but believe that he is now a SHIELD prisoner. So Dr. List ensues a challenge to the group that whoever manages to get SHIELD to come out of hiding will be new Whitehall.
There is an argument that erupts amongst our SHIELD agents about Bakshi but really it is about Tripp’s death. A shouting match occurs between Mack and Coulson and we see Skye becoming visibly upset as her vitals start to go off the charts and we also see the can of cactus juice starts to shake off the table but she manages to calm down enough without anyone noticing.
So the team starts to enact there Bakshi plan. Bakshi is going to be brought to Talbot and on the drive over, May and Coulson talk about not trusting those around Talbot and also that Whitehall is dead. This piece of information peaks Bakshi’s interest. However, the transport car gets hit by a van and presumably HYDRA agents start to attack May and Coulson. May being May manages to take out most of the HYDRA agents. When Coulson and May start to move Bakshi a lingering HYDRA agents confront them but when Coulson throws an over the top line of being captured, we know something is up as we see May and Coulson go down.
Bakshi’s rescuer is Hunter, using an American accent and after Bakshi makes contact with Bloom, Hunter turns on Bakshi ready to kill him. But Bakshi makes some grand promises so Hunter drives him to Bloom’s. The two arrive at Bloom’s mansion and Bakshi asks Hunter to wait outside and will call him when ready. While waiting, Bobbi enters the van, she had been tailing them, and Hunter wants to know what secret she and Mack have. Bobbi says they are in a support group together which Hunter actually swallows as the truth and teases her about it.
Inside Bloom’s mansion, it seems like the HYDRA council is about to eat each other as we see Bloom set in motion some sort of protocol where agents are alerted via watch to proceed. We see the banker, the Sheik and the Baroness all killed and presumably Dr. List too. Bakshi tries to get Hunter and Bobbi killed but Hunter presses the danger button in the car and manages to gun down their attackers. When the former couple enter the mansion, they take down Bloom and guards and take Bakshi to Talbot.
Back at the HQ, Simmons is back and sees that Raina has completely new DNA and believes that they should eliminate an alien beings, which include Raina. This stance seems to shock May, Coulson and even Skye.
Later, Fitz tells Skye that he fixed her biometric bracelet and it found that her heart beat 300 beats per minute during the earthquake, a rate that is Inhuman. Fitz realizes that Skye is the one that caused the earthquake that killed Tripp and we see her get so upset that the lamp in her room shatters. Fitz leaves and as Skye cleans the glass and cuts her hand. May and Simmons comes in and the three talk. May notices that Skye’s hand is blooding and asks what is wrong. Fitz comes back and covers for her says he was such a klutz that he broke the lamp. Fitz tells Simmons that Skye’s test results came back normal that she is fine. Everyone is relieved so quarantine is no longer needed. As Fitz sees to Skye’s hand, he tells her that he switched the blood samples with her before ones that the new ones are drastically different. Fitz promises to cover for Skye and even comforts her when she thinks something is wrong with her. Fitz proclaims nothing is wrong with but she is just different now.
We get a scene of Coulson visiting Tripp’s mom to tell her the devastating news of her son’s death and comforts the woman. Coulson spies a photograph of Tripp’s grandfather as a member of the Howling Commandoes.
While all this is happening, Raina walks into busy traffic in an attempt to kill herself. However, men with guns come out of SUVs and want to take her in. These are either HYDRA or SHIELD agents. However, Raina doesn’t want to go with them and says they will have to kill her. Before anything can happen, Raina is teleported away by Gordon, who calls her beautiful.
In the coda, we see the remote control Lola that Mack built scanning Coulson’s office and seems to find something in his desk. While the SHIELD agents share stories about Tripp, we see Bobbi talk to Mack and says the car found Fury’s tool box in Coulson’s desk. Pleased with this, Bobbi says she will reach out to their contact. What exactly do these two want with Fury’s tool kit and who is their contact?